6-30889209-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001297654.2(DDR1):c.196A>G(p.Ser66Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000096 ( 0 hom. )

Consequence

DDR1
NM_001297654.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.242

Variant links:

Genes affected

DDR1 (HGNC:2730): (discoidin domain receptor tyrosine kinase 1) Receptor tyrosine kinases play a key role in the communication of cells with their microenvironment. These kinases are involved in the regulation of cell growth, differentiation and metabolism. The protein encoded by this gene belongs to a subfamily of tyrosine kinase receptors with homology to Dictyostelium discoideum protein discoidin I in their extracellular domain, and that are activated by various types of collagen. Expression of this protein is restricted to epithelial cells, particularly in the kidney, lung, gastrointestinal tract, and brain. In addition, it has been shown to be significantly overexpressed in several human tumors. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

DDR1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.17468506).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDR1	NM_001297654.2 linkuse as main transcript	c.196A>G	p.Ser66Gly	missense_variant	4/18	ENST00000376568.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDR1	ENST00000376568.8 linkuse as main transcript	c.196A>G	p.Ser66Gly	missense_variant	4/18	1	NM_001297654.2	P1	Q08345-1

Frequencies

GnomAD3 genomes

AF:

0.0000855

AC:

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000290

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000811

AC:

AN:

246528

Hom.:

AF XY:

0.00

AC XY:

AN XY:

134384

show subpopulations

Gnomad AFR exome

AF:

0.000132

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000958

AC:

AN:

1460726

Hom.:

Cov.:

AF XY:

0.00000550

AC XY:

AN XY:

726678

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000497

GnomAD4 genome

AF:

0.0000855

AC:

AN:

152124

Hom.:

Cov.:

AF XY:

0.0000942

AC XY:

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.000290

Gnomad4 AMR

AF:

0.0000654

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.000136

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 26, 2021

The c.196A>G (p.S66G) alteration is located in exon 3 (coding exon 3) of the DDR1 gene. This alteration results from a A to G substitution at nucleotide position 196, causing the serine (S) at amino acid position 66 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.082

BayesDel_noAF

Benign

-0.11

Cadd

Pathogenic

Dann

Uncertain

0.99

DEOGEN2

Uncertain

0.59

D;T;D;.;.;.;T;T;.;D;.;D;T;.;D;.;D;.;.;T;T;D;D;.;T;T;D;D;.;.;T;.;.

Eigen

Benign

-0.31

Eigen_PC

Benign

-0.35

FATHMM_MKL

Benign

0.18

LIST_S2

Benign

0.86

D;D;.;D;D;.;D;D;D;D;.;.;D;D;.;D;D;.;.;D;D;.;.;.;T;.;D;D;D;.;.;.;D

M_CAP

Uncertain

0.17

MetaRNN

Benign

0.17

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Uncertain

0.43

MutationTaster

Benign

1.0

N;N;N;N;N;N;N;N;N;N;N;N

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-2.4

N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N

REVEL

Uncertain

0.40

Sift

Benign

0.077

T;D;D;D;D;T;D;D;D;D;T;D;D;D;D;D;D;T;T;T;T;D;D;T;D;D;D;D;D;T;T;D;D

Sift4G

Benign

0.30

T;T;T;T;T;T;T;D;D;T;T;T;D;T;T;D;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.98, 0.98, 0.96

.;.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;D;D;.;.;.;.;.;.;.;.;D;D

Vest4

0.16, 0.18, 0.21, 0.19, 0.18, 0.15, 0.15, 0.20, 0.13, 0.22, 0.16

MutPred

0.41

Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);.;Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);.;Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);Loss of phosphorylation at S66 (P = 0.0172);

MVP

0.91

MPC

0.46

ClinPred

0.14

GERP RS

2.4

Varity_R

0.42

gMVP

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.19

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over